[2026-06-08T08:47:44] Launching Arriba 2.4.0
[2026-06-08T08:47:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:58] Reading chimeric alignments from '659_ciJ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10251527)
[2026-06-08T08:54:35] Marking multi-mapping alignments (marked=6413907)
[2026-06-08T08:54:39] Detecting strandedness (reverse)
[2026-06-08T08:54:39] Assigning strands to alignments 
[2026-06-08T08:54:41] Annotating alignments 
[2026-06-08T08:55:15] Filtering duplicates (remaining=4288387)
[2026-06-08T08:55:21] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=4072344)
[2026-06-08T08:55:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4072344)
[2026-06-08T08:55:25] Filtering viral contigs with expression lower than the top 5 (remaining=4072344)
[2026-06-08T08:55:30] Filtering viral contigs with less than 5% coverage (remaining=4072344)
[2026-06-08T08:55:32] Estimating fragment length (mate gap mean=-87.3414, mate gap stddev=30.8232, read length mean=136.652)
[2026-06-08T08:55:32] Filtering read-through fragments with a distance <=10000bp (remaining=3835307)
[2026-06-08T08:55:35] Filtering inconsistently clipped mates (remaining=3783980)
[2026-06-08T08:55:37] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3641476)
[2026-06-08T08:55:41] Filtering fragments with small insert size (remaining=3641047)
[2026-06-08T08:55:43] Filtering alignments with long gaps (remaining=3641047)
[2026-06-08T08:55:45] Filtering fragments with both mates in the same gene (remaining=3640320)
[2026-06-08T08:55:48] Filtering fusions arising from hairpin structures (remaining=3472138)
[2026-06-08T08:55:50] Filtering reads with a mismatch p-value <=0.01 (remaining=1470683)
[2026-06-08T08:56:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=525843)
[2026-06-08T08:56:09] Finding fusions and counting supporting reads (total=445895)
[2026-06-08T08:56:24] Merging adjacent fusion breakpoints (remaining=441088)
[2026-06-08T08:56:26] Filtering multi-mapping fusions by alignment score and read support (remaining=277518)
[2026-06-08T08:57:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=275198)
[2026-06-08T08:57:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=143462)
[2026-06-08T08:57:07] Filtering fusions with <2 supporting reads (remaining=19488)
[2026-06-08T08:57:07] Filtering fusions with an e-value >=0.3 (remaining=7646)
[2026-06-08T08:57:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7681)
[2026-06-08T08:57:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7578)
[2026-06-08T08:57:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7580)
[2026-06-08T08:57:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4781)
[2026-06-08T08:57:17] Searching for fusions with spliced split reads (remaining=4858)
[2026-06-08T08:57:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=3189)
[2026-06-08T08:57:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3141)
[2026-06-08T08:57:23] Searching for fusions with >=4 spliced events (remaining=3489)
[2026-06-08T08:57:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1114)
[2026-06-08T08:57:40] Filtering fusions with anchors <=23nt (remaining=785)
[2026-06-08T08:57:40] Filtering end-to-end fusions with low support (remaining=749)
[2026-06-08T08:57:41] Filtering fusions with no coverage around the breakpoints (remaining=724)
[2026-06-08T08:57:41] Indexing gene sequences 
[2026-06-08T08:57:45] Filtering genes with >=30% identity (remaining=289)
[2026-06-08T08:57:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=172)
[2026-06-08T08:57:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=153)
[2026-06-08T08:57:50] Searching for additional isoforms (remaining=174)
[2026-06-08T08:57:51] Assigning confidence scores to events 
[2026-06-08T08:57:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:53] Writing fusions to file '659_ciJ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:57:55] Writing discarded fusions to file '659_ciJ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:17] Freeing resources
[2026-06-08T08:58:34] Done (elapsed time=00:10:50, CPU time=00:10:48, peak memory=14.8gb)